cellranger-atac mkref (1.2.0) Copyright (c) 2019 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Non-standard genome name detected, building custom reference... >>> Creating reference for GRCz11_v4.2.1_org <<< Creating new reference folder at /share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/GRCz11_v4.2.1_org Copying original fasta file into reference folder... done Generating samtools index... done Generating pyfasta indexes... Number of contigs: 998 Total genome size: 1373475517 done Copying original gene annotation file into reference folder... done Writing TSS and transcripts bed file... Parsed 87028 unique TSS and 100663 unique transcripts. done Generating bwa index (may take over an hour for a 3Gb genome)... [bwa_index] Pack FASTA... 20.59 sec [bwa_index] Construct BWT for the packed sequence... [BWTIncCreate] textLength=2746951034, availableWord=205285296 [BWTIncConstructFromPacked] 10 iterations done. 99999994 characters processed. [BWTIncConstructFromPacked] 20 iterations done. 199999994 characters processed. [BWTIncConstructFromPacked] 30 iterations done. 299999994 characters processed. [BWTIncConstructFromPacked] 40 iterations done. 399999994 characters processed. [BWTIncConstructFromPacked] 50 iterations done. 499999994 characters processed. [BWTIncConstructFromPacked] 60 iterations done. 599999994 characters processed. [BWTIncConstructFromPacked] 70 iterations done. 699999994 characters processed. [BWTIncConstructFromPacked] 80 iterations done. 799999994 characters processed. [BWTIncConstructFromPacked] 90 iterations done. 899999994 characters processed. [BWTIncConstructFromPacked] 100 iterations done. 999999994 characters processed. [BWTIncConstructFromPacked] 110 iterations done. 1099999994 characters processed. [BWTIncConstructFromPacked] 120 iterations done. 1199999994 characters processed. [BWTIncConstructFromPacked] 130 iterations done. 1299999994 characters processed. [BWTIncConstructFromPacked] 140 iterations done. 1399999994 characters processed. [BWTIncConstructFromPacked] 150 iterations done. 1499999994 characters processed. [BWTIncConstructFromPacked] 160 iterations done. 1599999994 characters processed. [BWTIncConstructFromPacked] 170 iterations done. 1699999994 characters processed. [BWTIncConstructFromPacked] 180 iterations done. 1799999994 characters processed. [BWTIncConstructFromPacked] 190 iterations done. 1899999994 characters processed. [BWTIncConstructFromPacked] 200 iterations done. 1999999994 characters processed. [BWTIncConstructFromPacked] 210 iterations done. 2099494330 characters processed. [BWTIncConstructFromPacked] 220 iterations done. 2190602426 characters processed. [BWTIncConstructFromPacked] 230 iterations done. 2271575530 characters processed. [BWTIncConstructFromPacked] 240 iterations done. 2343540618 characters processed. [BWTIncConstructFromPacked] 250 iterations done. 2407499370 characters processed. [BWTIncConstructFromPacked] 260 iterations done. 2464342042 characters processed. [BWTIncConstructFromPacked] 270 iterations done. 2514859930 characters processed. [BWTIncConstructFromPacked] 280 iterations done. 2559756378 characters processed. [BWTIncConstructFromPacked] 290 iterations done. 2599656394 characters processed. [BWTIncConstructFromPacked] 300 iterations done. 2635115610 characters processed. [BWTIncConstructFromPacked] 310 iterations done. 2666627818 characters processed. [BWTIncConstructFromPacked] 320 iterations done. 2694631930 characters processed. [BWTIncConstructFromPacked] 330 iterations done. 2719518026 characters processed. [BWTIncConstructFromPacked] 340 iterations done. 2741632810 characters processed. [bwt_gen] Finished constructing BWT in 343 iterations. [bwa_index] 1326.83 seconds elapse. [bwa_index] Update BWT... 16.68 sec [bwa_index] Pack forward-only FASTA... 13.66 sec [bwa_index] Construct SA from BWT and Occ... 351.53 sec [main] Version: 0.7.17-r1188 [main] CMD: bwa index /share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/GRCz11_v4.2.1_org/fasta/genome.fa [main] Real time: 1771.166 sec; CPU: 1729.317 sec done Copying original pfm file into reference folder... done Finishing up... Traceback (most recent call last): File "/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/bin/mkref", line 68, in main() File "/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/bin/mkref", line 62, in main reference_builder.build_reference() File "/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/lib/python/reference.py", line 548, in build_reference check_reference_format(self.ref_path) File "/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/cellranger-atac-1.2.0/cellranger-atac-cs/1.2.0/lib/python/preflights.py", line 200, in check_reference_format martian.exit(error_msg) File "/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/cellranger-atac-1.2.0/martian-cs/v3.2.4/adapters/python/martian.py", line 265, in exit _INSTANCE.metadata.write_assert(message) AttributeError: 'NoneType' object has no attribute 'metadata' ------------------------------------------------------------ Sender: LSF System Subject: Job 489463: in cluster Exited Job was submitted from host by user in cluster at Fri Dec 13 15:52:55 2019. Job was executed on host(s) , in queue , as user in cluster at Fri Dec 13 15:52:58 2019. was used as the home directory. was used as the working directory. Started at Fri Dec 13 15:52:58 2019. Terminated at Fri Dec 13 16:24:53 2019. Results reported at Fri Dec 13 16:24:53 2019. Your job looked like: ------------------------------------------------------------ # LSBATCH: User input cd /share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1 && export PATH=/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/cellranger-atac-1.2.0:/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/GRCz11_v4.2.1/cellranger-atac-1.2.0:/share/data/umw_biocore/genome_data/cellrangeratac/zebrafish/cellranger-atac-1.2.0:/usr/lib64/qt-3.3/bin:/lsf/9.1/linux2.6-glibc2.3-x86_64/etc:/lsf/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/ibutils/bin:/opt/dell/srvadmin/bin:/home/cjh/mplusdemo && cellranger-atac mkref GRCz11_v4.2.1_org --config config_org.txt ------------------------------------------------------------ Exited with exit code 1. Resource usage summary: CPU time : 1826.67 sec. Max Memory : 2047 MB Average Memory : 893.92 MB Total Requested Memory : 100048.00 MB Delta Memory : 98001.00 MB Max Swap : - Max Processes : 6 Max Threads : 7 Run time : 1914 sec. Turnaround time : 1918 sec. The output (if any) is above this job summary.